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Cloutier S, Reimer E, Khadka B, McCallum BD. Variations in exons 11 and 12 of the multi-pest resistance wheat gene Lr34 are independently additive for leaf rust resistance. FRONTIERS IN PLANT SCIENCE 2023; 13:1061490. [PMID: 36910459 PMCID: PMC9995823 DOI: 10.3389/fpls.2022.1061490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Characterization of germplasm collections for the wheat leaf rust gene Lr34 previously defined five haplotypes in spring wheat. All resistant lines had a 3-bp TTC deletion (null) in exon 11, resulting in the absence of a phenylalanine residue in the ABC transporter, as well as a single nucleotide C (Tyrosine in Lr34+) to T (Histidine in Lr34-) transition in exon 12. A rare haplotype present in Odesskaja 13 and Koktunkulskaja 332, both of intermediate rust resistance, had the 3-bp deletion typical of Lr34+ in exon 11 but the T nucleotide of Lr34- in exon 12. METHODS To quantify the role of each mutation in leaf rust resistance, Odesskaja 13 and Koktunkulskaja 332 were crossed to Thatcher and its near-isogenic line Thatcher-Lr34 (RL6058). Single seed descent populations were generated and evaluated for rust resistance in six different rust nurseries. RESULTS The Odesskaja 13 progeny with the TTC/T haplotype were susceptible with an average severity rating of 62.3%, the null/T haplotype progeny averaged 39.7% and the null/C haplotype was highly resistant, averaging 13.3% severity. The numbers for the Koktunkulskaja 332 crosses were similar with 63.5%, 43.5% and 23.7% severity ratings, respectively. Differences between all classes in all crosses were statistically significant, indicating that both mutations are independently additive for leaf rust resistance. The three-dimensional structural models of LR34 were used to analyze the locations and putative interference of both amino acids with the transport channel. Koktunkulskaja 332 also segregated for marker csLV46 which is linked to Lr46. Rust severity in lines with Lr34+ and csLV46+ had significantly lower rust severity ratings than those without, indicating the additivity of the two loci. DISCUSSION This has implications for the deployment of Lr34 in wheat cultivars and for the basic understanding of this important wheat multi-pest durable resistance gene.
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Affiliation(s)
- Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Elsa Reimer
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Bijendra Khadka
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Brent D. McCallum
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
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Dey D, Poudyal S, Rehman A, Hasan SS. Structural and biochemical insights into flavivirus proteins. Virus Res 2021; 296:198343. [PMID: 33607183 DOI: 10.1016/j.virusres.2021.198343] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 01/01/2023]
Abstract
Flaviviruses are the fastest spreading arthropod-borne viruses that cause severe symptoms such as hepatitis, hemorrhagic fever, encephalitis, and congenital deformities. Nearly 40 % of the entire human population is at risk of flavivirus epidemics. Yet, effective vaccination is restricted only to a few flaviviruses such as yellow fever and Japanese encephalitis viruses, and most recently for select cases of dengue virus infections. Despite the global spread of dengue virus, and emergence of new threats such as Zika virus and a new genotype of Japanese encephalitis virus, insights into flavivirus targets for potentially broad-spectrum vaccination are limited. In this review article, we highlight biochemical and structural differences in flavivirus proteins critical for virus assembly and host interactions. A comparative sequence analysis of pH-responsive properties of viral structural proteins identifies trends in conservation of complementary acidic-basic character between interacting viral structural proteins. This is highly relevant to the understanding of pH-sensitive differences in virus assembly in organelles such as neutral ER and acidic Golgi. Surface residues in viral interfaces identified by structural approaches are shown to demonstrate partial conservation, further reinforcing virus-specificity in assembly and interactions with host proteins. A comparative analysis of epitope conservation in emerging flaviviruses identifies therapeutic antibody candidates that have potential as broad spectrum anti-virals, thus providing a path towards development of vaccines.
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Affiliation(s)
- Debajit Dey
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene Street, Baltimore MD 21201, USA
| | - Shishir Poudyal
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette IN 47907, USA
| | - Asma Rehman
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene Street, Baltimore MD 21201, USA
| | - S Saif Hasan
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene Street, Baltimore MD 21201, USA; University of Maryland Marlene and Stewart Greenebaum Cancer Center, University of Maryland Medical Center, 22. S. Greene St. Baltimore MD 21201, USA; Center for Biomolecular Therapeutics, University of Maryland School of Medicine, 9600 Gudelsky Drive, Rockville MD 20850, USA.
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Yang C, Gong R, de Val N. Development of Neutralizing Antibodies against Zika Virus Based on Its Envelope Protein Structure. Virol Sin 2019; 34:168-174. [PMID: 31020573 PMCID: PMC6513807 DOI: 10.1007/s12250-019-00093-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/28/2019] [Indexed: 12/26/2022] Open
Abstract
As we know more about Zika virus (ZIKV), as well as its linkage to birth defects (microcephaly) and autoimmune neurological syndromes, we realize the importance of developing an efficient vaccine against it. Zika virus disease has affected many countries and is becoming a major public health concern. To deal with the infection of ZIKV, plenty of experiments have been done on selection of neutralizing antibodies that can target the envelope (E) protein on the surface of the virion. However, the existence of antibody-dependent enhancement (ADE) effect might limit the use of them as therapeutic candidates. In this review, we classify the neutralizing antibodies against ZIKV based on the epitopes and summarize the resolved structural information on antibody/antigen complex from X-ray crystallography and cryo-electron microscopy (cryo-EM), which might be useful for further development of potent neutralizing antibodies and vaccines toward clinical use.
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Affiliation(s)
- Chunpeng Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rui Gong
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
| | - Natalia de Val
- Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD, 21701, USA.
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4
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Zhao D, Liu Q, Huang X, Wang H, Han K, Yang J, Bi K, Liu Y, Zhang L, Li Y. Identification of determinants that mediate binding between Tembusu virus and the cellular receptor heat shock protein A9. J Vet Sci 2018; 19:528-535. [PMID: 29649860 PMCID: PMC6070589 DOI: 10.4142/jvs.2018.19.4.528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/16/2018] [Accepted: 03/20/2018] [Indexed: 12/19/2022] Open
Abstract
Heat shock protein A9 (HSPA9), a member of the heat shock protein family, is a putative receptor for Tembusu virus (TMUV). By using Western blot and co-immunoprecipitation assays, E protein domains I and II were identified as the functional domains that facilitate HSPA9 binding. Twenty-five overlapping peptides covering domain I and domain II sequences were synthesized and analyzed by using an HSPA9 binding assay. Two peptides showed the capability of binding to HSPA9. Dot blot assay of truncated peptides indicated that amino acid residues 19 to 22 and 245 to 252 of E protein constitute the minimal motifs required for TMUV binding to HSPA9. Importantly, peptides harboring those two minimal motifs could effectively inhibit TMUV infection. Our results provide insight into TMUV-receptor interaction, thereby creating opportunities for elucidating the mechanism of TMUV entry.
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Affiliation(s)
- Dongmin Zhao
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
| | - Qingtao Liu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
| | - Xinmei Huang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
| | - Huili Wang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
| | - Kaikai Han
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
| | - Jing Yang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
| | - Keran Bi
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
| | - Yuzhuo Liu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
| | - Lijiao Zhang
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
| | - Yin Li
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Veterinary Biological Engineering and Technology, Ministry of Agriculture, Nanjing 210014, China
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Tang H, Mori Y. Glycoproteins of HHV-6A and HHV-6B. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1045:145-165. [PMID: 29896667 DOI: 10.1007/978-981-10-7230-7_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Recently, human herpesvirus 6A and 6B (HHV-6A and HHV-6B) were classified into distinct species. Although these two viruses share many similarities, cell tropism is one of their striking differences, which is partially because of the difference in their entry machinery. Many glycoproteins of HHV-6A/B have been identified and analyzed in detail, especially in their functions during entry process into host cells. Some of these glycoproteins were unique to HHV-6A/B. The cellular factors associated with these viral glycoproteins (or glycoprotein complex) were also identified in recent years. Detailed interaction analyses were also conducted, which could partially prove the difference of entry machinery in these two viruses. Although there are still issues that should be addressed, all the knowledges that have been earned in recent years could not only help us to understand these viruses' entry mechanism well but also would contribute to the development of the therapy and/or prophylaxis methods for HHV-6A/B-associated diseases.
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Affiliation(s)
- Huamin Tang
- Department of Immunology, Nanjing Medical University, Nanjing, China.
| | - Yasuko Mori
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
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6
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New insights into flavivirus biology: the influence of pH over interactions between prM and E proteins. J Comput Aided Mol Des 2017; 31:1009-1019. [DOI: 10.1007/s10822-017-0076-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 10/09/2017] [Indexed: 10/18/2022]
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7
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Molecular association of herpes simplex virus type 1 glycoprotein E with membrane protein Us9. Arch Virol 2016; 161:3203-13. [PMID: 27568015 DOI: 10.1007/s00705-016-3028-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 08/22/2016] [Indexed: 01/20/2023]
Abstract
Herpes simplex virus type 1 (HSV-1) glycoprotein E (gE), glycoprotein I (gI), and Us9 promote efficient anterograde axonal transport of virus from the neuron cytoplasm to the axon terminus. HSV-1 and PRV gE and gI form a heterodimer that is required for anterograde transport, but an association that includes Us9 has not been demonstrated. NS-gE380 is an HSV-1 mutant that has five amino acids inserted after gE residue 380, rendering it defective in anterograde axonal transport. We demonstrated that gE, gI and Us9 form a trimolecular complex in Vero cells infected with NS-gE380 virus in which gE binds to both Us9 and gI. We detected the complex using immunoprecipitation with anti-gE or anti-gI monoclonal antibodies in the presence of ionic detergents. Under these conditions, Us9 did not associate with gE in cells infected with wild-type HSV-1; however, using a nonionic detergent, TritonX-100, an association between Us9 and gE was detected in immunoprecipitates of both wild-type and NS-gE380-infected cells. The results suggest that the interaction between Us9 and gE is weak and disrupted by ionic detergents in wild-type infected cells. We postulate that the tight interaction between Us9 and gE leads to the anterograde spread defect in the NS-gE380 virus.
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8
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Fields W, Kielian M. Interactions involved in pH protection of the alphavirus fusion protein. Virology 2015; 486:173-9. [PMID: 26433749 DOI: 10.1016/j.virol.2015.08.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 08/25/2015] [Indexed: 11/18/2022]
Abstract
The alphavirus membrane protein E1 mediates low pH-triggered fusion of the viral and endosome membranes during virus entry. During virus biogenesis E1 associates as a heterodimer with the transmembrane protein p62. Late in the secretory pathway, cellular furin cleaves p62 to the mature E2 protein and a peripheral protein E3. E3 remains bound to E2 at low pH, stabilizing the heterodimer and thus protecting E1 from the acidic pH of the secretory pathway. Release of E3 at neutral pH then primes the virus for fusion during entry. Here we used site-directed mutagenesis and revertant analysis to define residues important for the interactions at the E3-E2 interface. Our data identified a key residue, E2 W235, which was required for E1 pH protection and alphavirus production. Our data also suggest additional residues on E3 and E2 that affect their interacting surfaces and thus influence the pH protection of E1 during alphavirus exit.
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Affiliation(s)
- Whitney Fields
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Margaret Kielian
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA.
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9
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Receptor-Guided De Novo Design of Dengue Envelope Protein Inhibitors. Appl Biochem Biotechnol 2015; 177:861-78. [PMID: 26299376 DOI: 10.1007/s12010-015-1784-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 07/27/2015] [Indexed: 10/23/2022]
Abstract
Inhibitor design associated with the dynamics of dengue envelope protein at pre-fusion stage is a prominent strategy to interfere fusion transition of dengue virus with the host cell membrane. Receptor-guided de novo inhibitors were designed based on the knowledge of co-crystallized detergent, β-octyl glucoside. Pharmacophore features distribution showed the preference of aromatic groups with H bonding features connected to aliphatic bulky group as the skeleton for inhibitor design. Molecular dynamic simulations revealed (2R)-2-[(6-amino-1-oxohexan-2-yl)amino]-4-[6-(4-phenylpiperidine-1-yl)-1,2-benzoxazol-3-yl]butanoate as the probable binder which developed extensive conservative interactions despite the local pocket residues movements especially from kl β-hairpin, the key structural unit for initiating conformational changes required for fusion transition. The electronic and hydrophobic potentials also indicated that butanoate molecule as the initial lead for envelope protein inhibitors.
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10
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Valéry C, Deville-Foillard S, Lefebvre C, Taberner N, Legrand P, Meneau F, Meriadec C, Delvaux C, Bizien T, Kasotakis E, Lopez-Iglesias C, Gall A, Bressanelli S, Le Du MH, Paternostre M, Artzner F. Atomic view of the histidine environment stabilizing higher-pH conformations of pH-dependent proteins. Nat Commun 2015; 6:7771. [PMID: 26190377 PMCID: PMC4518280 DOI: 10.1038/ncomms8771] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 06/09/2015] [Indexed: 11/17/2022] Open
Abstract
External stimuli are powerful tools that naturally control protein assemblies and functions. For example, during viral entry and exit changes in pH are known to trigger large protein conformational changes. However, the molecular features stabilizing the higher pH structures remain unclear. Here we elucidate the conformational change of a self-assembling peptide that forms either small or large nanotubes dependent on the pH. The sub-angstrom high-pH peptide structure reveals a globular conformation stabilized through a strong histidine-serine H-bond and a tight histidine-aromatic packing. Lowering the pH induces histidine protonation, disrupts these interactions and triggers a large change to an extended β-sheet-based conformation. Re-visiting available structures of proteins with pH-dependent conformations reveals both histidine-containing aromatic pockets and histidine-serine proximity as key motifs in higher pH structures. The mechanism discovered in this study may thus be generally used by pH-dependent proteins and opens new prospects in the field of nanomaterials. In biological systems, large pH-induced conformational changes can be observed in certain proteins, a phenomenon poorly understood at the molecular level. Here the authors describe a peptide with the ability to self-organize into either small or large nanotubes in a pH-dependent manner and detail the mechanism driving the transition.
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Affiliation(s)
- Céline Valéry
- 1] Biomolecular Interaction Centre, School of Biological Sciences, University of Canterbury, 8140 Christchurch, New zealand [2] Ipsen, 5 Avenue du Canada, 91940 Les Ulis, France
| | - Stéphanie Deville-Foillard
- 1] Ipsen, 5 Avenue du Canada, 91940 Les Ulis, France [2] CEA, Institute of Biology and Technologies of Saclay, 91191 CEA-Saclay, France [3] Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91191 CEA-Saclay, Gif sur Yvette, France
| | - Christelle Lefebvre
- CNRS, UMR 6251, Institut de Physique de Rennes, 263 av. Général Leclerc, Université Rennes I, 35042 Rennes Cedex, France
| | | | | | | | - Cristelle Meriadec
- CNRS, UMR 6251, Institut de Physique de Rennes, 263 av. Général Leclerc, Université Rennes I, 35042 Rennes Cedex, France
| | - Camille Delvaux
- 1] CEA, Institute of Biology and Technologies of Saclay, 91191 CEA-Saclay, France [2] Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91191 CEA-Saclay, Gif sur Yvette, France
| | - Thomas Bizien
- CNRS, UMR 6251, Institut de Physique de Rennes, 263 av. Général Leclerc, Université Rennes I, 35042 Rennes Cedex, France
| | - Emmanouil Kasotakis
- 1] CEA, Institute of Biology and Technologies of Saclay, 91191 CEA-Saclay, France [2] Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91191 CEA-Saclay, Gif sur Yvette, France
| | - Carmen Lopez-Iglesias
- Cryo-Electron Microscopy Unit. Scientific and Tecnological Centers of the University of Barcelona, E-08028 Barcelona, Spain
| | - Andrew Gall
- 1] CEA, Institute of Biology and Technologies of Saclay, 91191 CEA-Saclay, France [2] Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91191 CEA-Saclay, Gif sur Yvette, France
| | - Stéphane Bressanelli
- 1] CEA, Institute of Biology and Technologies of Saclay, 91191 CEA-Saclay, France [2] Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91191 CEA-Saclay, Gif sur Yvette, France
| | - Marie-Hélène Le Du
- 1] CEA, Institute of Biology and Technologies of Saclay, 91191 CEA-Saclay, France [2] Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91191 CEA-Saclay, Gif sur Yvette, France
| | - Maïté Paternostre
- 1] CEA, Institute of Biology and Technologies of Saclay, 91191 CEA-Saclay, France [2] Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, 91191 CEA-Saclay, Gif sur Yvette, France
| | - Franck Artzner
- CNRS, UMR 6251, Institut de Physique de Rennes, 263 av. Général Leclerc, Université Rennes I, 35042 Rennes Cedex, France
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11
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Unexpected structural features of the hepatitis C virus envelope protein 2 ectodomain. J Virol 2014; 88:10280-8. [PMID: 24991010 DOI: 10.1128/jvi.00874-14] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hepatitis C virus (HCV), a member of the family Flaviviridae, is a leading cause of chronic liver disease and cancer. Recent advances in HCV therapeutics have resulted in improved cure rates, but an HCV vaccine is not available and is urgently needed to control the global pandemic. Vaccine development has been hampered by the lack of high-resolution structural information for the two HCV envelope glycoproteins, E1 and E2. Recently, Kong and coworkers (Science 342:1090-1094, 2013, doi:10.1126/science.1243876) and Khan and coworkers (Nature 509[7500]:381-384, 2014, doi:10.1038/nature13117) independently determined the structure of the HCV E2 ectodomain core with some unexpected and informative results. The HCV E2 ectodomain core features a globular architecture with antiparallel β-sheets forming a central β sandwich. The residues comprising the epitopes of several neutralizing and nonneutralizing human monoclonal antibodies were also determined, which is an essential step toward obtaining a fine map of the human humoral response to HCV. Also clarified were the regions of E2 that directly bind CD81, an important HCV cellular receptor. While it has been widely assumed that HCV E2 is a class II viral fusion protein (VFP), the newly determined structure suggests that the HCV E2 ectodomain shares structural and functional similarities only with domain III of class II VFPs. The new structural determinations suggest that the HCV glycoproteins use a different mechanism than that used by class II fusion proteins for cell fusion.
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12
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Leonova GN, Maystrovskaya OS, Kondratov IG, Takashima I, Belikov SI. The nature of replication of tick-borne encephalitis virus strains isolated from residents of the Russian Far East with inapparent and clinical forms of infection. Virus Res 2014; 189:34-42. [PMID: 24747117 DOI: 10.1016/j.virusres.2014.04.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 04/03/2014] [Accepted: 04/06/2014] [Indexed: 11/30/2022]
Abstract
We describe the biological properties and molecular characteristics of complete genomes of 33 tick-borne encephalitis virus (TBEV) strains that induced different forms of infection, from inapparent to severe focal ones resulting in fatal outcome. Hemagglutinating activity of Oshima-like strains was higher at pH 5.8, while activity of Sofjin- and Senhzang-like strains were higher at pH 6.2 and 6.8, respectively. We determined susceptibility of porcine kidney (PK) cell cultures to these TBEV strains by cytopathic effect (CPE), plaque formation, and size of plaques. The clinical TBEV strains had higher virus titers both in tissue culture infectious dose 50(TCID50) and in plaque-forming unit (PFU) titers and larger plaques than the inapparent strains. A comparison of virus multiplication kinetics by PFU in culture fluid with kinetics of ELISA antigen and hemagglutinin accumulation suggested a different mechanism of interaction between these virus strains and PK cells at the initial stage of cell infection.
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Affiliation(s)
- Galina N Leonova
- Institute of Epidemiology and Microbiology, Siberian Branch of Russian Academy of Medical Sciences, Vladivostok, Russian Federation.
| | - Olga S Maystrovskaya
- Institute of Epidemiology and Microbiology, Siberian Branch of Russian Academy of Medical Sciences, Vladivostok, Russian Federation
| | - Ilya G Kondratov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russian Federation
| | - Ikuo Takashima
- Graduate School of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Sergei I Belikov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russian Federation
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Fuzo CA, Degrève L. The pH dependence of flavivirus envelope protein structure: insights from molecular dynamics simulations. J Biomol Struct Dyn 2013; 32:1563-74. [DOI: 10.1080/07391102.2013.827132] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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A key interaction between the alphavirus envelope proteins responsible for initial dimer dissociation during fusion. J Virol 2013; 87:3774-81. [PMID: 23325694 DOI: 10.1128/jvi.03310-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Alphaviruses such as Semliki Forest virus (SFV) are enveloped viruses whose surface is covered by an organized lattice composed of trimers of E2-E1 heterodimers. The E1 envelope protein, a class II fusion protein, contains the hydrophobic fusion loop and refolds to drive virus fusion with the endosome membrane. The E2 protein is synthesized as a precursor p62, whose processing by furin primes the heterodimer for dissociation during virus entry. Dissociation of the E2-E1 heterodimer is an essential step during low-pH-triggered fusion, while the dissociation of the immature p62-E1 dimer is relatively pH resistant. Previous structural studies described an "acid-sensitive region" in E2 that becomes disordered at low pH. Within this region, the conserved E2 H170 is in position to form a hydrogen bond with the underlying E1 S57. Here we experimentally tested the role of this interaction in regulating dimer dissociation in mature and immature virus. Alanine substitutions of E1 S57 and E2 H170 destabilized the heterodimer and produced a higher pH threshold for exposure of the E1 fusion loop and for fusion of the immature virus. E1 S57K or S57D mutations were lethal and caused transport and assembly defects that were partially abrogated by neutralization of the exocytic pathway. The lethal phenotype of E1 S57K was rescued by second-site mutations at E2 H170/M171. Together, our results define a key role for the E1 S57-E2 H170 interaction in dimer stability and the pH dependence of fusion and provide evidence for stepwise dissociation of the E2-E1 dimer at low pH.
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Abstract
One of the factors limiting the search of new compounds based on the structure of target proteins involved in diseases is the limited amount of target structural information. Great advances in the search for lead compounds could be achieved to find new cavities in protein structures that are generated using well established computational chemistry tools. In the case of dengue, the discovery of pockets in the crystallographic structure of the E protein has contributed to the search for lead compounds aimed at interfering in conformational transitions involved in the pH-dependent fusion process. This is a complex mechanism triggered by the acid pH of the endosomes that leads to the initial changes in the E protein assembly at the virus surface. In the present work, an arrangement of three ectodomain portions of the E protein present on the surface of the mature dengue virus was studied through long all-atom molecular dynamics simulations with explicit solvent. In order to identify new pockets and to evaluate the influence of the acid pH on these pockets, the physiological neutral pH conditions and the acid pH of the endosomes that trigger the fusion process were modeled. Several pockets presenting pH-dependent characteristics were found in the contact regions between the chains. Pockets at the protein-protein interfaces induced by a monomer in another monomer were also found. Some of the pockets are good candidates for the design of lead compounds that could interfere in the rearrangements in E proteins along the fusion process contributing to the development of specific inhibitors of the dengue disease.
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Japanese encephalitis virus enters rat neuroblastoma cells via a pH-dependent, dynamin and caveola-mediated endocytosis pathway. J Virol 2012; 86:13407-22. [PMID: 23015720 DOI: 10.1128/jvi.00903-12] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Japanese encephalitis virus (JEV) is a mosquito-borne flavivirus and one of the most common agents of viral encephalitis. The infectious entry process of JEV into host cells remains largely unknown. Here, we present a systemic study concerning the cellular entry mechanism of JEV to B104 rat neuroblastoma cells. It was observed that JEV internalization was inhibited by chloroquine and ammonium chloride, both of which can elevate the pH of acidic organelles. However, JEV entry was not affected by chlorpromazine, overexpression of a dominant-negative form of EPS 15 protein, or silencing of the clathrin heavy chain by small interfering RNA (siRNA). These results suggested that JEV entry depended on the acidic intracellular pH but was independent of clathrin. We found that endocytosis of JEV was dependent on membrane cholesterol and was inhibited by inactivation of caveolin-1 with siRNA or dominant-negative mutants. It was also shown, by using the inhibitor dynasore, the K44A mutant, and specific siRNA, that dynamin was required for JEV entry. Phagocytosis or macropinocytosis did not play a role in JEV internalization. In addition, we showed that JEV entry into the neuroblastoma cells is not virus strain specific by assessing the effect of the pharmacological inhibitors on the internalization of JEV belonging to different genotypes. Taken together, our results demonstrate that JEV enters B104 cells through a dynamin-dependent caveola-mediated uptake with a pH-dependent step, which is distinct from the clathrin-mediated endocytosis used by most flaviviruses.
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Soares ROS, Caliri A. Stereochemical features of the envelope protein Domain III of dengue virus reveals putative antigenic site in the five-fold symmetry axis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:221-30. [PMID: 23009809 DOI: 10.1016/j.bbapap.2012.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2012] [Revised: 09/07/2012] [Accepted: 09/11/2012] [Indexed: 11/18/2022]
Abstract
We bring to attention a characteristic parasitic pattern present in the dengue virus: it undergoes several intensive thermodynamic variations due to host environmental changes, from a vector's digestive tract, through the human bloodstream and intracellular medium. Comparatively, among the known dengue serotypes, we evaluate the effects that these medium variations may induce to the overall structural characteristics of the Domain III of the envelope (E) protein, checking for stereochemical congruences that could lead to the identification of immunologic relevant regions. We used molecular dynamics and principal component analysis to study the protein in solution, for all four dengue serotypes, under distinct pH and temperature. We stated that, while the core of Domain III is remarkably rigid and effectively unaffected by most of the mentioned intensive variations, the loops account for major and distinguishable flexibilities. Therefore, the rigidity of the Domain III core provides a foothold that projects specifically two of these high flexible loop regions towards the inner face of the envelope pores, which are found at every five-fold symmetry axis of the icosahedron-shaped mature virus. These loops bear a remarkable low identity though with high occurrence of ionizable residues, including histidines. Such stereochemical properties can provide very particular serotype-specific electrostatic surface patterns, suggesting a viral fingerprint region, on which other specific molecules and ions can establish chemical interactions in an induced fit mechanism. We assert that the proposed regions share enough relevant features to qualify for further immunologic and pharmacologic essays, such as target peptide synthesis and phage display using dengue patients' sera.
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Affiliation(s)
- R O S Soares
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café, S/N. 14040-903, Ribeirão Preto, São Paulo, Brazil.
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18
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Koellhoffer JF, Malashkevich VN, Harrison JS, Toro R, Bhosle RC, Chandran K, Almo SC, Lai JR. Crystal structure of the Marburg virus GP2 core domain in its postfusion conformation. Biochemistry 2012; 51:7665-75. [PMID: 22935026 DOI: 10.1021/bi300976m] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Marburg virus (MARV) and Ebola virus (EBOV) are members of the family Filoviridae ("filoviruses") and cause severe hemorrhagic fever with human case fatality rates of up to 90%. Filovirus infection requires fusion of the host cell and virus membranes, a process that is mediated by the envelope glycoprotein (GP). GP contains two subunits, the surface subunit (GP1), which is responsible for cell attachment, and the transmembrane subunit (GP2), which catalyzes membrane fusion. The GP2 ectodomain contains two heptad repeat regions, N-terminal and C-terminal (NHR and CHR, respectively), that adopt a six-helix bundle during the fusion process. The refolding of this six-helix bundle provides the thermodynamic driving force to overcome barriers associated with membrane fusion. Here we report the crystal structure of the MARV GP2 core domain in its postfusion (six-helix bundle) conformation at 1.9 Å resolution. The MARV GP2 core domain backbone conformation is virtually identical to that of EBOV GP2 (reported previously), and consists of a central NHR core trimeric coiled coil packed against peripheral CHR α-helices and an intervening loop and helix-turn-helix segments. We previously reported that the stability of the MARV GP2 postfusion structure is highly pH-dependent, with increasing stability at lower pH [Harrison, J. S., Koellhoffer, J. K., Chandran, K., and Lai, J. R. (2012) Biochemistry51, 2515-2525]. We hypothesized that this pH-dependent stability provides a mechanism for conformational control such that the postfusion six-helix bundle is promoted in the environments of appropriately mature endosomes. In this report, a structural rationale for this pH-dependent stability is described and involves a high-density array of core and surface acidic side chains at the midsection of the structure, termed the "anion stripe". In addition, many surface-exposed salt bridges likely contribute to the stabilization of the postfusion structure at low pH. These results provide structural insights into the mechanism of MARV GP2-mediated membrane fusion.
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Affiliation(s)
- Jayne F Koellhoffer
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States
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19
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Rücker P, Wieninger SA, Ullmann GM, Sticht H. pH-dependent molecular dynamics of vesicular stomatitis virus glycoprotein G. Proteins 2012; 80:2601-13. [PMID: 22806964 DOI: 10.1002/prot.24145] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Revised: 06/18/2012] [Accepted: 07/05/2012] [Indexed: 02/06/2023]
Abstract
Vesicular stomatitis virus glycoprotein G (VSV-G) belongs to a new class of viral fusion proteins (Class III). The structure of VSV-G has been solved in two different conformations and fusion is known to be triggered by low pH. To investigate Class III fusion mechanisms, molecular dynamics simulations were performed on the VSV-G prefusion structure in two different protonation states: at physiological pH (pH 7) and low pH present in the endosome (pH 5). Domain IV containing the fusion loops, which need to interact with the target membrane, exhibits the highest mobility. Energetic analyses revealed weakened interaction between Domain IV and the protein core at pH 5, which can be attributed to two pairs of structurally neighboring conserved and differentially protonated residues in the Domain IV-core interface. Energetic calculations also demonstrated that the interaction between the subunits in the core of the trimeric VSV-G is strengthened at pH 5, mainly due to newly formed interactions between the C-terminal loop of Domain II and the N-terminus of the adjacent subunit. A pair of interacting residues in this interface that is affected by differential protonation was shown to be the main effectors of this phenomenon. The results of this study thus enhance the mechanistic understanding of the effects of protonation changes in VSV-G.
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Affiliation(s)
- Pia Rücker
- Bioinformatics, Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
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20
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Vázquez-Calvo A, Saiz JC, McCullough KC, Sobrino F, Martín-Acebes MA. Acid-dependent viral entry. Virus Res 2012; 167:125-37. [PMID: 22683298 DOI: 10.1016/j.virusres.2012.05.024] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 05/28/2012] [Accepted: 05/29/2012] [Indexed: 12/21/2022]
Abstract
Virus infection of host cells requires that entry into the cell results in efficient genome release leading to translation and replication. These initial steps revolving around the entry and genomic release processes are crucial for viral progeny generation. Despite the variety of receptors used by viruses to initiate entry, evidence from both enveloped and non-enveloped viral infections is highlighting the important role played by intracellular acidic compartments in the entry of many viruses. These compartments provide connecting nodes within the endocytic network, presenting multiple viral internalization pathways. Endosomal compartments employing an internal acidic pH can trigger molecular mechanisms leading to disassembly of viral particles, thus providing appropriate genome delivery. Accordingly, viruses have evolved to select optimal intracellular conditions for promoting efficient genome release, leading to propagation of the infectious agent. This review will address the implications of cellular compartment involvement in virus infectious processes, and the roles played by the viruses' own machinery, including pH sensing mechanisms and the methodologies applied for studying acid-dependent viral entry into host cells.
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Affiliation(s)
- Angela Vázquez-Calvo
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Cantoblanco, 28049 Madrid, Spain.
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21
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Autographa californica multiple nucleopolyhedrovirus GP64 protein: roles of histidine residues in triggering membrane fusion and fusion pore expansion. J Virol 2011; 85:12492-504. [PMID: 21937651 DOI: 10.1128/jvi.05153-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Autographa californica multiple nucleopolyhedrovirus (AcMNPV) GP64 protein mediates membrane fusion during entry. Fusion results from a low-pH-triggered conformational change in GP64 and subsequent interactions with the membrane bilayers. The low-pH sensor and trigger of the conformational change are not known, but histidine residues are implicated because the pK(a) of histidine is near the threshold for triggering fusion by GP64. We used alanine substitutions to examine the roles of all individual and selected clusters of GP64 histidine residues in triggering and mediating fusion by GP64. Three histidine residues (H152, H155, and H156), located in fusion loop 2, were identified as important for membrane fusion. These three histidine residues were important for efficient pore expansion but were not required for the pH-triggered conformational change. In contrast, a cluster of three histidine residues (H245, H304, and H430) located near the base of the central coiled coil was identified as a putative sensor for low pH. Three alanine substitutions in cluster H245/H304/H430 resulted in dramatically reduced membrane fusion and the apparent loss of the prefusion conformation at neutral pH. Thus, the H245/H304/H430 cluster of histidines may function or participate as a pH sensor by stabilizing the prefusion structure of GP64.
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22
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Structural characterization of an early fusion intermediate of influenza virus hemagglutinin. J Virol 2011; 85:5172-82. [PMID: 21367895 DOI: 10.1128/jvi.02430-10] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The hemagglutinin (HA) envelope protein of influenza virus mediates viral entry through membrane fusion in the acidic environment of the endosome. Crystal structures of HA in pre- and postfusion states have laid the foundation for proposals for a general fusion mechanism for viral envelope proteins. The large-scale conformational rearrangement of HA at low pH is triggered by a loop-to-helix transition of an interhelical loop (B loop) within the fusion domain and is often referred to as the "spring-loaded" mechanism. Although the receptor-binding HA1 subunit is believed to act as a "clamp" to keep the B loop in its metastable prefusion state at neutral pH, the "pH sensors" that are responsible for the clamp release and the ensuing structural transitions have remained elusive. Here we identify a mutation in the HA2 fusion domain from the influenza virus H2 subtype that stabilizes the HA trimer in a prefusion-like state at and below fusogenic pH. Crystal structures of this putative early intermediate state reveal reorganization of ionic interactions at the HA1-HA2 interface at acidic pH and deformation of the HA1 membrane-distal domain. Along with neutralization of glutamate residues on the B loop, these changes cause a rotation of the B loop and solvent exposure of conserved phenylalanines, which are key residues at the trimer interface of the postfusion structure. Thus, our study reveals the possible initial structural event that leads to release of the B loop from its prefusion conformation, which is aided by unexpected structural changes within the membrane-distal HA1 domain at low pH.
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Smit JM, Moesker B, Rodenhuis-Zybert I, Wilschut J. Flavivirus cell entry and membrane fusion. Viruses 2011; 3:160-171. [PMID: 22049308 PMCID: PMC3206597 DOI: 10.3390/v3020160] [Citation(s) in RCA: 221] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 02/10/2011] [Accepted: 02/10/2011] [Indexed: 12/26/2022] Open
Abstract
Flaviviruses, such as dengue virus and West Nile virus, are enveloped viruses that infect cells through receptor-mediated endocytosis and fusion from within acidic endosomes. The cell entry process of flaviviruses is mediated by the viral E glycoprotein. This short review will address recent advances in the understanding of flavivirus cell entry with specific emphasis on the recent study of Zaitseva and coworkers, indicating that anionic lipids might play a crucial role in the fusion process of dengue virus [1].
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Affiliation(s)
- Jolanda M. Smit
- Department of Medical Microbiology, Molecular Virology Section, University Medical Center Groningen, University of Groningen, PO Box 30.001, 9700 RB Groningen, The Netherlands; E-Mails: (B.M.); (I.R.-Z.); (J.W.)
| | - Bastiaan Moesker
- Department of Medical Microbiology, Molecular Virology Section, University Medical Center Groningen, University of Groningen, PO Box 30.001, 9700 RB Groningen, The Netherlands; E-Mails: (B.M.); (I.R.-Z.); (J.W.)
| | - Izabela Rodenhuis-Zybert
- Department of Medical Microbiology, Molecular Virology Section, University Medical Center Groningen, University of Groningen, PO Box 30.001, 9700 RB Groningen, The Netherlands; E-Mails: (B.M.); (I.R.-Z.); (J.W.)
| | - Jan Wilschut
- Department of Medical Microbiology, Molecular Virology Section, University Medical Center Groningen, University of Groningen, PO Box 30.001, 9700 RB Groningen, The Netherlands; E-Mails: (B.M.); (I.R.-Z.); (J.W.)
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Mechanism of inhibition of enveloped virus membrane fusion by the antiviral drug arbidol. PLoS One 2011; 6:e15874. [PMID: 21283579 PMCID: PMC3026800 DOI: 10.1371/journal.pone.0015874] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Accepted: 11/28/2010] [Indexed: 12/13/2022] Open
Abstract
The broad-spectrum antiviral arbidol (Arb) inhibits cell entry of enveloped viruses by blocking viral fusion with host cell membrane. To better understand Arb mechanism of action, we investigated its interactions with phospholipids and membrane peptides. We demonstrate that Arb associates with phospholipids in the micromolar range. NMR reveals that Arb interacts with the polar head-group of phospholipid at the membrane interface. Fluorescence studies of interactions between Arb and either tryptophan derivatives or membrane peptides reconstituted into liposomes show that Arb interacts with tryptophan in the micromolar range. Interestingly, apparent binding affinities between lipids and tryptophan residues are comparable with those of Arb IC50 of the hepatitis C virus (HCV) membrane fusion. Since tryptophan residues of membrane proteins are known to bind preferentially at the membrane interface, these data suggest that Arb could increase the strength of virus glycoprotein's interactions with the membrane, due to a dual binding mode involving aromatic residues and phospholipids. The resulting complexation would inhibit the expected viral glycoprotein conformational changes required during the fusion process. Our findings pave the way towards the design of new drugs exhibiting Arb-like interfacial membrane binding properties to inhibit early steps of virus entry, i.e., attractive targets to combat viral infection.
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25
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Martín-Acebes MA, Saiz JC. A West Nile virus mutant with increased resistance to acid-induced inactivation. J Gen Virol 2011; 92:831-40. [PMID: 21228127 DOI: 10.1099/vir.0.027185-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
West Nile virus (WNV) is a mosquito-borne flavivirus responsible for epidemics of febrile illness, meningitis, encephalitis and flaccid paralysis. WNV gains entry into host cells through endocytosis. The acid pH inside endosomes triggers rapid conformational rearrangements of the flavivirus envelope (E) glycoprotein that result in fusion of the endosomal membrane with the virion envelope. Conformational rearrangements of the E glycoprotein can be induced by acid exposure in solution in the absence of target membranes, thus causing a loss of infectivity. Following a genetic approach to study this process, a WNV mutant with increased resistance to acid-induced inactivation was isolated and its complete genome was sequenced. A single amino acid substitution, T70I, in the E glycoprotein was found to be responsible for the increased acid resistance, which was linked to an increase in the sensitivity of infection to the chemical rise of endosomal pH, suggesting that the mutant required a more acid pH inside the endosomes for fusion. No alterations in viral infection kinetics, plaque size or induced mortality rates in mice of the mutant were noted. However, by means of virus competition assays, a reduction in viral fitness under standard culture conditions was observed for the mutant. These results provide new evidence of the adaptive flexibility to environmental factors--pH variation in this case--of WNV populations. Implications of the T70I replacement on the E glycoprotein structure-function relationship are discussed.
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Affiliation(s)
- Miguel A Martín-Acebes
- Departamento de Biotecnología, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain
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26
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Kaufmann B, Rossmann MG. Molecular mechanisms involved in the early steps of flavivirus cell entry. Microbes Infect 2010; 13:1-9. [PMID: 20869460 DOI: 10.1016/j.micinf.2010.09.005] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 08/31/2010] [Accepted: 09/01/2010] [Indexed: 12/31/2022]
Abstract
Flaviviruses enter their host cells by receptor-mediated endocytosis, a well-orchestrated process of receptor recognition, penetration and uncoating. Recent findings on these early steps in the life cycle of flaviviruses are the focus of this review.
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Affiliation(s)
- Bärbel Kaufmann
- Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054, USA
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27
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Prakash MK, Barducci A, Parrinello M. Probing the mechanism of pH-induced large-scale conformational changes in dengue virus envelope protein using atomistic simulations. Biophys J 2010; 99:588-94. [PMID: 20643078 PMCID: PMC2905125 DOI: 10.1016/j.bpj.2010.04.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Revised: 03/29/2010] [Accepted: 04/05/2010] [Indexed: 10/19/2022] Open
Abstract
One of the key steps in the infection of the cell by dengue virus is a pH-induced conformational change of the viral envelope proteins. These envelope proteins undergo a rearrangement from a dimer to a trimer, with large conformational changes in the monomeric unit. In this article, metadynamics simulations were used to enable us to understand the mechanism of these large-scale changes in the monomer. By using all-atom, explicit solvent simulations of the monomers, the stability of the protein structure is studied under low and high pH conditions. Free energy profiles obtained along appropriate collective coordinates demonstrate that pH affects the domain interface in both the conformations of E monomer, stabilizing one and destabilizing the other. These simulations suggest a mechanism with an intermediate detached state between the two monomeric structures. Using further analysis, we comment on the key residue interactions responsible for the instability and the pH-sensing role of a histidine that could not otherwise be studied experimentally. The insights gained from this study and methodology can be extended for studying similar mechanisms in the E proteins of the other members of class II flavivirus family.
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Affiliation(s)
- Meher K. Prakash
- Department of Chemistry and Applied Biosciences, ETH Zurich, Lugano, Switzerland
| | - Alessandro Barducci
- Department of Chemistry and Applied Biosciences, ETH Zurich, Lugano, Switzerland
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28
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Small interference RNA profiling reveals the essential role of human membrane trafficking genes in mediating the infectious entry of dengue virus. Virol J 2010; 7:24. [PMID: 20122152 PMCID: PMC2825209 DOI: 10.1186/1743-422x-7-24] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Accepted: 02/01/2010] [Indexed: 12/23/2022] Open
Abstract
Background Dengue virus (DENV) is the causative agent of Dengue fever and the life-threatening Dengue Haemorrhagic fever or Dengue shock syndrome. In the absence of anti-viral agents or vaccine, there is an urgent need to develop an effective anti-viral strategy against this medically important viral pathogen. The initial interplay between DENV and the host cells may represent one of the potential anti-viral targeting sites. Currently the involvements of human membrane trafficking host genes or factors that mediate the infectious cellular entry of dengue virus are not well defined. Results In this study, we have used a targeted small interfering RNA (siRNA) library to identify and profile key cellular genes involved in processes of endocytosis, cytoskeletal dynamics and endosome trafficking that are important and essential for DENV infection. The infectious entry of DENV into Huh7 cells was shown to be potently inhibited by siRNAs targeting genes associated with clathrin-mediated endocytosis. The important role of clathrin-mediated endocytosis was confirmed by the expression of well-characterized dominant-negative mutants of genes in this pathway and by using the clathrin endocytosis inhibitor chlorpromazine. Furthermore, DENV infection was shown to be sensitive to the disruption of human genes in regulating the early to late endosomal trafficking as well as the endosomal acidic pH. The importance and involvement of both actin and microtubule dynamics in mediating the infectious entry of DENV was also revealed in this study. Conclusions Together, the findings from this study have provided a detail profiling of the human membrane trafficking cellular genes and the mechanistic insight into the interplay of these host genes with DENV to initiate an infection, hence broadening our understanding on the entry pathway of this medically important viral pathogen. These data may also provide a new potential avenue for development of anti-viral strategies and treatment of DENV infection.
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Stiasny K, Fritz R, Pangerl K, Heinz FX. Molecular mechanisms of flavivirus membrane fusion. Amino Acids 2009; 41:1159-63. [PMID: 19882217 DOI: 10.1007/s00726-009-0370-4] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Accepted: 10/12/2009] [Indexed: 01/09/2023]
Abstract
Flaviviruses comprise a number of important human pathogens including yellow fever, dengue, West Nile, Japanese encephalitis and tick-borne encephalitis viruses. They are small enveloped viruses that enter cells by receptor-mediated endocytosis and release their nucleocapsid into the cytoplasm by fusing their membrane with the endosomal membrane. The fusion event is triggered by the acidic pH in the endosome and is mediated by the major envelope protein E. Based on the atomic structures of the pre- and post-fusion conformations of E, a fusion model has been proposed that includes several steps leading from the metastable assembly of E at the virion surface to membrane merger and fusion pore formation trough conversion of E into a stable trimeric post-fusion conformation. Using recombinant subviral particles of tick-borne encephalitis virus as a model, we have defined individual steps of the molecular processes underlying the flavivirus fusion mechanisms. This includes the identification of a conserved histidine as being part of the pH sensor in the fusion protein that responds to the acidic pH and thus initiates the structural transitions driving fusion.
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Affiliation(s)
- Karin Stiasny
- Institute of Virology, Medical University of Vienna, AT, Austria.
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30
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The hepatitis C virus and its hepatic environment: a toxic but finely tuned partnership. Biochem J 2009; 423:303-14. [PMID: 19807698 DOI: 10.1042/bj20091000] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Twenty years after its discovery, HCV (hepatitis C virus) still infects 170 million people worldwide and cannot be properly treated due to the lack of efficient medication. Its life cycle must be better understood to develop targeted pharmacological arsenals. HCV is an enveloped virus bearing two surface glycoproteins, E1 and E2. It only infects humans through blood transmission, and hepatocytes are its only target cells. Hepatic trabeculae are formed by hepatocyte rows surrounded by sinusoid capillaries, irrigating hepatic cells. Hepatocytes are polarized and have basolateral and apical poles, separated by tight junctions in contact with blood and bile respectively. In blood, HCV remains in contact with lipoproteins. It then navigates through hepatic microenvironment and extracellular matrix, composed of glycosaminoglycans and proteins. HCV then encounters the hepatocyte basolateral membrane, where it interacts with its entry factors: the low-density lipoprotein receptor, CD81 tetraspanin, and the high-density lipoprotein (scavenger) receptor SR-BI (scavenger receptor BI). How these molecules interact with HCV remains unclear; however, a tentative sequence of events has been proposed. Two essential factors of HCV entry are the tight junction proteins claudin-1 and occludin. Cell polarity therefore seems to be a key for HCV entry. This raises several exciting questions on the HCV internalization pathway. Clathrin-dependent endocytosis is probably the route of HCV transport to intracellular compartments, and the ultimate step of its entry is fusion, which probably takes place within endosomes. The mechanisms of HCV membrane fusion are still unclear, notably the nature of the fusion proteins is unknown and the contribution of HCV-associated lipoproteins to this event is currently under investigation.
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31
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Sánchez-San Martín C, Liu CY, Kielian M. Dealing with low pH: entry and exit of alphaviruses and flaviviruses. Trends Microbiol 2009; 17:514-21. [PMID: 19796949 DOI: 10.1016/j.tim.2009.08.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2009] [Revised: 08/06/2009] [Accepted: 08/17/2009] [Indexed: 10/20/2022]
Abstract
The alphaviruses and flaviviruses include many important human pathogens, such as the dengue, West Nile, and Chikungunya viruses. These enveloped viruses infect cells by a membrane fusion reaction triggered by the low pH in endosomes. Fusion is mediated by viral membrane proteins through their acid-dependent conversion from a dimer on the virus surface to a homotrimer inserted into the host cell membrane. Here we review recent studies on the regulatory mechanisms that silence these fusion proteins during virus exit and that sense low pH and mediate protein refolding during virus entry. We discuss results using truncated proteins to dissect the fusion reaction, and future research directions including the development of antiviral therapies against these medically important viruses.
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